2025-09-07T20:28:37,361 Created temporary directory: /tmp/pip-build-tracker-kopn3982 2025-09-07T20:28:37,361 Initialized build tracking at /tmp/pip-build-tracker-kopn3982 2025-09-07T20:28:37,362 Created build tracker: /tmp/pip-build-tracker-kopn3982 2025-09-07T20:28:37,362 Entered build tracker: /tmp/pip-build-tracker-kopn3982 2025-09-07T20:28:37,362 Created temporary directory: /tmp/pip-wheel-jmlhl5rb 2025-09-07T20:28:37,365 Created temporary directory: /tmp/pip-ephem-wheel-cache-81v6goqh 2025-09-07T20:28:37,420 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-09-07T20:28:37,422 2 location(s) to search for versions of nwalign: 2025-09-07T20:28:37,422 * https://pypi.org/simple/nwalign/ 2025-09-07T20:28:37,422 * https://www.piwheels.org/simple/nwalign/ 2025-09-07T20:28:37,423 Fetching project page and analyzing links: https://pypi.org/simple/nwalign/ 2025-09-07T20:28:37,423 Getting page https://pypi.org/simple/nwalign/ 2025-09-07T20:28:37,424 Found index url https://pypi.org/simple/ 2025-09-07T20:28:37,572 Fetched page https://pypi.org/simple/nwalign/ as application/vnd.pypi.simple.v1+json 2025-09-07T20:28:37,575 Found link https://files.pythonhosted.org/packages/c8/26/9ca7ef2ddd1680a8a56c8b9c04f0b97f6c5a4b1fdd32f4795022317823a8/nwalign-0.1.tar.gz (from https://pypi.org/simple/nwalign/), version: 0.1 2025-09-07T20:28:37,576 Found link https://files.pythonhosted.org/packages/a1/c8/1e9a68782c95d700d695c8b1f3a8934e1072e8ed60491e430896b834f961/nwalign-0.1.1.tar.gz (from https://pypi.org/simple/nwalign/), version: 0.1.1 2025-09-07T20:28:37,576 Found link https://files.pythonhosted.org/packages/b0/88/af6b4592f61add748195ef777dce0892bde1e2520d81b92e80e76b86deb4/nwalign-0.1.2.tar.gz (from https://pypi.org/simple/nwalign/), version: 0.1.2 2025-09-07T20:28:37,577 Found link https://files.pythonhosted.org/packages/e4/56/1e74d542efb45570042356a81bbad81cc6adc23bb4d5fcf6fd642ec2658b/nwalign-0.1.3.tar.gz (from https://pypi.org/simple/nwalign/), version: 0.1.3 2025-09-07T20:28:37,577 Found link https://files.pythonhosted.org/packages/5d/35/f962c0a6d870ea7ff96ba2465b276054192d36597cee2832972a0736bbb1/nwalign-0.2.tar.gz (from https://pypi.org/simple/nwalign/), version: 0.2 2025-09-07T20:28:37,578 Found link https://files.pythonhosted.org/packages/d1/2e/44355ba45f5a7ae0f0e1dcce833952470a95353669307a9a90affcbb757e/nwalign-0.3.0.tar.gz (from https://pypi.org/simple/nwalign/), version: 0.3.0 2025-09-07T20:28:37,578 Found link https://files.pythonhosted.org/packages/33/f9/96fdb624719c4122d559af37275c9af258ca9b1b93411e16ef0ec4899c3f/nwalign-0.3.1.tar.gz (from https://pypi.org/simple/nwalign/), version: 0.3.1 2025-09-07T20:28:37,579 Fetching project page and analyzing links: https://www.piwheels.org/simple/nwalign/ 2025-09-07T20:28:37,580 Getting page https://www.piwheels.org/simple/nwalign/ 2025-09-07T20:28:37,582 Found index url https://www.piwheels.org/simple/ 2025-09-07T20:28:37,691 Fetched page https://www.piwheels.org/simple/nwalign/ as text/html 2025-09-07T20:28:37,698 Skipping link: No binaries permitted for nwalign: https://archive1.piwheels.org/simple/nwalign/nwalign-0.3.1-cp35-cp35m-linux_armv7l.whl#sha256=0e50aba5718a22fcc30c7d356e6cbca9f721c91d12ab32e7778624dca0940847 (from https://www.piwheels.org/simple/nwalign/) 2025-09-07T20:28:37,698 Skipping link: No binaries permitted for nwalign: https://archive1.piwheels.org/simple/nwalign/nwalign-0.3.1-cp35-cp35m-linux_armv6l.whl#sha256=0e50aba5718a22fcc30c7d356e6cbca9f721c91d12ab32e7778624dca0940847 (from https://www.piwheels.org/simple/nwalign/) 2025-09-07T20:28:37,698 Skipping link: No binaries permitted for nwalign: https://archive1.piwheels.org/simple/nwalign/nwalign-0.3.1-cp34-cp34m-linux_armv7l.whl#sha256=ae6113c797139e0f35a03f3ff8af1b2ff22e983e866116804cdb2e04fcf66cf2 (from https://www.piwheels.org/simple/nwalign/) 2025-09-07T20:28:37,699 Skipping link: No binaries permitted for nwalign: 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(from https://www.piwheels.org/simple/nwalign/) 2025-09-07T20:28:37,699 Skipping link: No binaries permitted for nwalign: https://archive1.piwheels.org/simple/nwalign/nwalign-0.3.1-cp39-cp39-linux_armv7l.whl#sha256=08fb1551c85e0ecfdd72b0c2f3e03b9a0de96b8531202e5ff0b2b6fa1a560e43 (from https://www.piwheels.org/simple/nwalign/) 2025-09-07T20:28:37,699 Skipping link: No binaries permitted for nwalign: https://archive1.piwheels.org/simple/nwalign/nwalign-0.3.0-cp34-cp34m-linux_armv7l.whl#sha256=0f9707e25f4cca1595233e0e171c833a750fad16671b0c75c995f09e74df93fe (from https://www.piwheels.org/simple/nwalign/) 2025-09-07T20:28:37,700 Skipping link: No binaries permitted for nwalign: https://archive1.piwheels.org/simple/nwalign/nwalign-0.3.0-cp34-cp34m-linux_armv6l.whl#sha256=0f9707e25f4cca1595233e0e171c833a750fad16671b0c75c995f09e74df93fe (from https://www.piwheels.org/simple/nwalign/) 2025-09-07T20:28:37,700 Skipping link: No binaries permitted for nwalign: 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(from https://www.piwheels.org/simple/nwalign/) 2025-09-07T20:28:37,701 Skipping link: No binaries permitted for nwalign: https://archive1.piwheels.org/simple/nwalign/nwalign-0.2-cp35-cp35m-linux_armv6l.whl#sha256=51218ba0b2cac7da2369f816741091a1ca6655f6803e0ee1cb1cb78d1433f306 (from https://www.piwheels.org/simple/nwalign/) 2025-09-07T20:28:37,701 Skipping link: No binaries permitted for nwalign: https://archive1.piwheels.org/simple/nwalign/nwalign-0.2-cp34-cp34m-linux_armv7l.whl#sha256=f87e3ddff26114d9035b65a473f6c962e80a383b56607581149c97e329b3160a (from https://www.piwheels.org/simple/nwalign/) 2025-09-07T20:28:37,701 Skipping link: No binaries permitted for nwalign: https://archive1.piwheels.org/simple/nwalign/nwalign-0.2-cp34-cp34m-linux_armv6l.whl#sha256=f87e3ddff26114d9035b65a473f6c962e80a383b56607581149c97e329b3160a (from https://www.piwheels.org/simple/nwalign/) 2025-09-07T20:28:37,701 Skipping link: No binaries permitted for nwalign: https://archive1.piwheels.org/simple/nwalign/nwalign-0.2-cp37-cp37m-linux_armv7l.whl#sha256=f8cf67c435c305698af9aaea9170c1a6e255630b6589b6409d2c2b633939c01e (from https://www.piwheels.org/simple/nwalign/) 2025-09-07T20:28:37,701 Skipping link: No binaries permitted for nwalign: https://archive1.piwheels.org/simple/nwalign/nwalign-0.2-cp37-cp37m-linux_armv6l.whl#sha256=f8cf67c435c305698af9aaea9170c1a6e255630b6589b6409d2c2b633939c01e (from https://www.piwheels.org/simple/nwalign/) 2025-09-07T20:28:37,701 Skipping link: No binaries permitted for nwalign: https://archive1.piwheels.org/simple/nwalign/nwalign-0.2-cp39-cp39-linux_armv6l.whl#sha256=631f718358e76db5bc00a55370722902bb2031198826fbaf7a18f644c9a9e35f (from https://www.piwheels.org/simple/nwalign/) 2025-09-07T20:28:37,702 Skipping link: No binaries permitted for nwalign: https://archive1.piwheels.org/simple/nwalign/nwalign-0.2-cp39-cp39-linux_armv7l.whl#sha256=631f718358e76db5bc00a55370722902bb2031198826fbaf7a18f644c9a9e35f (from https://www.piwheels.org/simple/nwalign/) 2025-09-07T20:28:37,702 Skipping link: No binaries permitted for nwalign: https://archive1.piwheels.org/simple/nwalign/nwalign-0.1.3-cp35-cp35m-linux_armv7l.whl#sha256=e65315f5a29a7907ad4e0c9e28f2c81cd8f2a401632c114520ef48eaed3aa67d (from https://www.piwheels.org/simple/nwalign/) 2025-09-07T20:28:37,702 Skipping link: No binaries permitted for nwalign: https://archive1.piwheels.org/simple/nwalign/nwalign-0.1.3-cp35-cp35m-linux_armv6l.whl#sha256=e65315f5a29a7907ad4e0c9e28f2c81cd8f2a401632c114520ef48eaed3aa67d (from https://www.piwheels.org/simple/nwalign/) 2025-09-07T20:28:37,702 Skipping link: No binaries permitted for nwalign: https://archive1.piwheels.org/simple/nwalign/nwalign-0.1.3-cp34-cp34m-linux_armv7l.whl#sha256=059f73659cca427340d71fee5bfdf4e6479b7ba5ca5cd884941a1fa939573541 (from https://www.piwheels.org/simple/nwalign/) 2025-09-07T20:28:37,702 Skipping link: No binaries permitted for nwalign: 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https://archive1.piwheels.org/simple/nwalign/nwalign-0.1.2-cp34-cp34m-linux_armv7l.whl#sha256=43be14b0f5dfcd08d82b07636ce240399e1daaff6888cef7d9a902d38cfec888 (from https://www.piwheels.org/simple/nwalign/) 2025-09-07T20:28:37,703 Skipping link: No binaries permitted for nwalign: https://archive1.piwheels.org/simple/nwalign/nwalign-0.1.2-cp34-cp34m-linux_armv6l.whl#sha256=43be14b0f5dfcd08d82b07636ce240399e1daaff6888cef7d9a902d38cfec888 (from https://www.piwheels.org/simple/nwalign/) 2025-09-07T20:28:37,703 Skipping link: No binaries permitted for nwalign: https://archive1.piwheels.org/simple/nwalign/nwalign-0.1.1-cp34-cp34m-linux_armv7l.whl#sha256=0c8103577d0ab325258569e3f899576b2aa71d77af8cb6f3bee13aaa92370e63 (from https://www.piwheels.org/simple/nwalign/) 2025-09-07T20:28:37,703 Skipping link: No binaries permitted for nwalign: https://archive1.piwheels.org/simple/nwalign/nwalign-0.1.1-cp34-cp34m-linux_armv6l.whl#sha256=0c8103577d0ab325258569e3f899576b2aa71d77af8cb6f3bee13aaa92370e63 (from https://www.piwheels.org/simple/nwalign/) 2025-09-07T20:28:37,703 Skipping link: No binaries permitted for nwalign: https://archive1.piwheels.org/simple/nwalign/nwalign-0.1.1-cp35-cp35m-linux_armv6l.whl#sha256=05231f91c31665fc5a1c4039f2e36013fd1b49b5f38108f750af1aaf8858179b (from https://www.piwheels.org/simple/nwalign/) 2025-09-07T20:28:37,703 Skipping link: No binaries permitted for nwalign: https://archive1.piwheels.org/simple/nwalign/nwalign-0.1.1-cp35-cp35m-linux_armv7l.whl#sha256=05231f91c31665fc5a1c4039f2e36013fd1b49b5f38108f750af1aaf8858179b (from https://www.piwheels.org/simple/nwalign/) 2025-09-07T20:28:37,704 Skipping link: No binaries permitted for nwalign: https://archive1.piwheels.org/simple/nwalign/nwalign-0.1-cp35-cp35m-linux_armv7l.whl#sha256=6d0d1ff20e0a0cf071f3edb683e564e5795b6f14f356bde26acdd74fc0eb9d30 (from https://www.piwheels.org/simple/nwalign/) 2025-09-07T20:28:37,704 Skipping link: No binaries permitted for nwalign: https://archive1.piwheels.org/simple/nwalign/nwalign-0.1-cp35-cp35m-linux_armv6l.whl#sha256=6d0d1ff20e0a0cf071f3edb683e564e5795b6f14f356bde26acdd74fc0eb9d30 (from https://www.piwheels.org/simple/nwalign/) 2025-09-07T20:28:37,704 Skipping link: No binaries permitted for nwalign: https://archive1.piwheels.org/simple/nwalign/nwalign-0.1-cp34-cp34m-linux_armv7l.whl#sha256=33f737806954650dec90b3e358b6ef762bb5757b3184c24e8769b0feb3d4f5e1 (from https://www.piwheels.org/simple/nwalign/) 2025-09-07T20:28:37,704 Skipping link: No binaries permitted for nwalign: https://archive1.piwheels.org/simple/nwalign/nwalign-0.1-cp34-cp34m-linux_armv6l.whl#sha256=33f737806954650dec90b3e358b6ef762bb5757b3184c24e8769b0feb3d4f5e1 (from https://www.piwheels.org/simple/nwalign/) 2025-09-07T20:28:37,704 Skipping link: not a file: https://www.piwheels.org/simple/nwalign/ 2025-09-07T20:28:37,704 Skipping link: not a file: https://pypi.org/simple/nwalign/ 2025-09-07T20:28:37,729 Given no hashes to check 1 links for project 'nwalign': discarding no candidates 2025-09-07T20:28:37,730 Collecting nwalign==0.1 2025-09-07T20:28:37,731 Created temporary directory: /tmp/pip-unpack-gqrj52xk 2025-09-07T20:28:37,870 Downloading nwalign-0.1.tar.gz (42 kB) 2025-09-07T20:28:37,905 Added nwalign==0.1 from https://files.pythonhosted.org/packages/c8/26/9ca7ef2ddd1680a8a56c8b9c04f0b97f6c5a4b1fdd32f4795022317823a8/nwalign-0.1.tar.gz to build tracker '/tmp/pip-build-tracker-kopn3982' 2025-09-07T20:28:37,906 Running setup.py (path:/tmp/pip-wheel-jmlhl5rb/nwalign_0f5f0cbb29734c8d8106745a44654ca4/setup.py) egg_info for package nwalign 2025-09-07T20:28:37,906 Created temporary directory: /tmp/pip-pip-egg-info-x_r7kss7 2025-09-07T20:28:37,906 Preparing metadata (setup.py): started 2025-09-07T20:28:37,907 Running command python setup.py egg_info 2025-09-07T20:28:38,868 /usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'test_suite' 2025-09-07T20:28:38,868 warnings.warn(msg) 2025-09-07T20:28:39,269 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-07T20:28:39,270 !! 2025-09-07T20:28:39,270 ******************************************************************************** 2025-09-07T20:28:39,270 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-07T20:28:39,270 License :: OSI Approved :: BSD License 2025-09-07T20:28:39,270 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-07T20:28:39,270 ******************************************************************************** 2025-09-07T20:28:39,270 !! 2025-09-07T20:28:39,271 self._finalize_license_expression() 2025-09-07T20:28:39,343 running egg_info 2025-09-07T20:28:39,416 creating /tmp/pip-pip-egg-info-x_r7kss7/nwalign.egg-info 2025-09-07T20:28:39,416 writing /tmp/pip-pip-egg-info-x_r7kss7/nwalign.egg-info/PKG-INFO 2025-09-07T20:28:39,418 writing dependency_links to /tmp/pip-pip-egg-info-x_r7kss7/nwalign.egg-info/dependency_links.txt 2025-09-07T20:28:39,418 writing entry points to /tmp/pip-pip-egg-info-x_r7kss7/nwalign.egg-info/entry_points.txt 2025-09-07T20:28:39,419 writing requirements to /tmp/pip-pip-egg-info-x_r7kss7/nwalign.egg-info/requires.txt 2025-09-07T20:28:39,419 writing top-level names to /tmp/pip-pip-egg-info-x_r7kss7/nwalign.egg-info/top_level.txt 2025-09-07T20:28:39,419 writing manifest file '/tmp/pip-pip-egg-info-x_r7kss7/nwalign.egg-info/SOURCES.txt' 2025-09-07T20:28:39,637 reading manifest file '/tmp/pip-pip-egg-info-x_r7kss7/nwalign.egg-info/SOURCES.txt' 2025-09-07T20:28:39,640 writing manifest file '/tmp/pip-pip-egg-info-x_r7kss7/nwalign.egg-info/SOURCES.txt' 2025-09-07T20:28:39,777 Preparing metadata (setup.py): finished with status 'done' 2025-09-07T20:28:39,782 Source in /tmp/pip-wheel-jmlhl5rb/nwalign_0f5f0cbb29734c8d8106745a44654ca4 has version 0.1, which satisfies requirement nwalign==0.1 from https://files.pythonhosted.org/packages/c8/26/9ca7ef2ddd1680a8a56c8b9c04f0b97f6c5a4b1fdd32f4795022317823a8/nwalign-0.1.tar.gz 2025-09-07T20:28:39,782 Removed nwalign==0.1 from https://files.pythonhosted.org/packages/c8/26/9ca7ef2ddd1680a8a56c8b9c04f0b97f6c5a4b1fdd32f4795022317823a8/nwalign-0.1.tar.gz from build tracker '/tmp/pip-build-tracker-kopn3982' 2025-09-07T20:28:39,785 Created temporary directory: /tmp/pip-unpack-4vwj4vkj 2025-09-07T20:28:39,786 Created temporary directory: /tmp/pip-unpack-67ubjfpn 2025-09-07T20:28:39,786 Building wheels for collected packages: nwalign 2025-09-07T20:28:39,787 Created temporary directory: /tmp/pip-wheel-vxa1tynf 2025-09-07T20:28:39,787 DEPRECATION: Building 'nwalign' using the legacy setup.py bdist_wheel mechanism, which will be removed in a future version. pip 25.3 will enforce this behaviour change. A possible replacement is to use the standardized build interface by setting the `--use-pep517` option, (possibly combined with `--no-build-isolation`), or adding a `pyproject.toml` file to the source tree of 'nwalign'. Discussion can be found at https://github.com/pypa/pip/issues/6334 2025-09-07T20:28:39,788 Building wheel for nwalign (setup.py): started 2025-09-07T20:28:39,789 Destination directory: /tmp/pip-wheel-vxa1tynf 2025-09-07T20:28:39,789 Running command python setup.py bdist_wheel 2025-09-07T20:28:40,684 /usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'test_suite' 2025-09-07T20:28:40,684 warnings.warn(msg) 2025-09-07T20:28:41,079 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-07T20:28:41,080 !! 2025-09-07T20:28:41,080 ******************************************************************************** 2025-09-07T20:28:41,080 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-07T20:28:41,080 License :: OSI Approved :: BSD License 2025-09-07T20:28:41,080 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-07T20:28:41,080 ******************************************************************************** 2025-09-07T20:28:41,081 !! 2025-09-07T20:28:41,081 self._finalize_license_expression() 2025-09-07T20:28:41,081 running bdist_wheel 2025-09-07T20:28:41,448 running build 2025-09-07T20:28:41,448 running build_ext 2025-09-07T20:28:41,777 building 'nwalign' extension 2025-09-07T20:28:41,778 creating build/temp.linux-armv7l-cpython-313 2025-09-07T20:28:41,779 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/local/lib/python3.13/dist-packages/numpy/_core/include -I. -I/usr/include/python3.13 -c nwalign.c -o build/temp.linux-armv7l-cpython-313/nwalign.o 2025-09-07T20:28:42,226 nwalign.c: In function ‘__pyx_pf_7nwalign_read_matrix’: 2025-09-07T20:28:42,227 nwalign.c:1025:15: error: implicit declaration of function ‘PyEval_CallObjectWithKeywords’ [-Wimplicit-function-declaration] 2025-09-07T20:28:42,227 1025 | __pyx_t_6 = PyEval_CallObjectWithKeywords(((PyObject *)((PyObject*)__pyx_ptype_5numpy_ndarray)), ((PyObject *)__pyx_t_1), ((PyObject *)__pyx_1)); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 99; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-07T20:28:42,227 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-07T20:28:42,229 nwalign.c:1025:13: error: assignment to ‘PyObject *’ {aka ‘struct _object *’} from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 2025-09-07T20:28:42,229 1025 | __pyx_t_6 = PyEval_CallObjectWithKeywords(((PyObject *)((PyObject*)__pyx_ptype_5numpy_ndarray)), ((PyObject *)__pyx_t_1), ((PyObject *)__pyx_1)); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 99; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-07T20:28:42,229 | ^ 2025-09-07T20:28:42,235 nwalign.c:1142:37: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘Py_ssize_t’ {aka ‘int’} [-Wsign-compare] 2025-09-07T20:28:42,235 1142 | for (__pyx_t_12 = 0; __pyx_t_12 < __pyx_t_4; __pyx_t_12+=1) { 2025-09-07T20:28:42,235 | ^ 2025-09-07T20:28:42,238 nwalign.c:1205:29: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘Py_ssize_t’ {aka ‘int’} [-Wsign-compare] 2025-09-07T20:28:42,238 1205 | if (unlikely(!(__pyx_v_ai == __pyx_t_4))) { 2025-09-07T20:28:42,238 | ^~ 2025-09-07T20:28:42,238 nwalign.c:206:41: note: in definition of macro ‘unlikely’ 2025-09-07T20:28:42,238 206 | #define unlikely(x) __builtin_expect(!!(x), 0) 2025-09-07T20:28:42,238 | ^ 2025-09-07T20:28:42,241 nwalign.c:793:14: warning: variable ‘__pyx_bshape_1_a’ set but not used [-Wunused-but-set-variable] 2025-09-07T20:28:42,242 793 | Py_ssize_t __pyx_bshape_1_a = 0; 2025-09-07T20:28:42,242 | ^~~~~~~~~~~~~~~~ 2025-09-07T20:28:42,242 nwalign.c:792:14: warning: variable ‘__pyx_bshape_0_a’ set but not used [-Wunused-but-set-variable] 2025-09-07T20:28:42,243 792 | Py_ssize_t __pyx_bshape_0_a = 0; 2025-09-07T20:28:42,243 | ^~~~~~~~~~~~~~~~ 2025-09-07T20:28:42,247 nwalign.c: In function ‘__pyx_f_7nwalign_global_align’: 2025-09-07T20:28:42,249 nwalign.c:1623:13: error: assignment to ‘PyObject *’ {aka ‘struct _object *’} from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 2025-09-07T20:28:42,249 1623 | __pyx_t_5 = PyEval_CallObjectWithKeywords(__pyx_t_2, ((PyObject *)__pyx_t_4), ((PyObject *)__pyx_1)); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 147; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-07T20:28:42,249 | ^ 2025-09-07T20:28:42,253 nwalign.c:1678:13: error: assignment to ‘PyObject *’ {aka ‘struct _object *’} from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 2025-09-07T20:28:42,253 1678 | __pyx_t_3 = PyEval_CallObjectWithKeywords(__pyx_t_5, ((PyObject *)__pyx_t_2), ((PyObject *)__pyx_1)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 148; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-07T20:28:42,253 | ^ 2025-09-07T20:28:42,257 nwalign.c:1733:13: error: assignment to ‘PyObject *’ {aka ‘struct _object *’} from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 2025-09-07T20:28:42,258 1733 | __pyx_t_4 = PyEval_CallObjectWithKeywords(__pyx_t_3, ((PyObject *)__pyx_t_5), ((PyObject *)__pyx_1)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 149; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-07T20:28:42,258 | ^ 2025-09-07T20:28:42,267 nwalign.c:1962:13: error: assignment to ‘PyObject *’ {aka ‘struct _object *’} from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 2025-09-07T20:28:42,267 1962 | __pyx_t_3 = PyEval_CallObjectWithKeywords(__pyx_t_4, ((PyObject *)__pyx_t_2), ((PyObject *)__pyx_1)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 164; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-07T20:28:42,267 | ^ 2025-09-07T20:28:42,272 nwalign.c:2020:13: error: assignment to ‘PyObject *’ {aka ‘struct _object *’} from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 2025-09-07T20:28:42,272 2020 | __pyx_t_3 = PyEval_CallObjectWithKeywords(__pyx_t_5, ((PyObject *)__pyx_t_4), ((PyObject *)__pyx_1)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 165; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-07T20:28:42,272 | ^ 2025-09-07T20:28:42,278 nwalign.c:2212:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2025-09-07T20:28:42,278 2212 | if (!(__pyx_v_ii == -1)) { 2025-09-07T20:28:42,278 | ^~ 2025-09-07T20:28:42,281 nwalign.c:2213:36: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2025-09-07T20:28:42,281 2213 | __pyx_t_25 = (__pyx_v_jj == -1); 2025-09-07T20:28:42,281 | ^~ 2025-09-07T20:28:42,284 nwalign.c:2215:36: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2025-09-07T20:28:42,284 2215 | __pyx_t_25 = (__pyx_v_ii == -1); 2025-09-07T20:28:42,284 | ^~ 2025-09-07T20:28:42,286 nwalign.c:2226:36: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2025-09-07T20:28:42,286 2226 | __pyx_t_25 = (__pyx_v_ii == -1); 2025-09-07T20:28:42,286 | ^~ 2025-09-07T20:28:42,308 nwalign.c:2236:26: error: implicit declaration of function ‘PyString_FromStringAndSize’; did you mean ‘PyBytes_FromStringAndSize’? [-Wimplicit-function-declaration] 2025-09-07T20:28:42,308 2236 | __pyx_t_26 = PyString_FromStringAndSize((&__pyx_v_ci), ((size_t)1)); 2025-09-07T20:28:42,308 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-07T20:28:42,308 | PyBytes_FromStringAndSize 2025-09-07T20:28:42,311 nwalign.c:2236:24: error: assignment to ‘PyObject *’ {aka ‘struct _object *’} from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 2025-09-07T20:28:42,311 2236 | __pyx_t_26 = PyString_FromStringAndSize((&__pyx_v_ci), ((size_t)1)); 2025-09-07T20:28:42,311 | ^ 2025-09-07T20:28:42,316 nwalign.c:2291:36: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2025-09-07T20:28:42,316 2291 | __pyx_t_25 = (__pyx_v_jj == -1); 2025-09-07T20:28:42,316 | ^~ 2025-09-07T20:28:42,319 nwalign.c:2301:24: error: assignment to ‘PyObject *’ {aka ‘struct _object *’} from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 2025-09-07T20:28:42,319 2301 | __pyx_t_26 = PyString_FromStringAndSize((&__pyx_v_cj), ((size_t)1)); 2025-09-07T20:28:42,319 | ^ 2025-09-07T20:28:42,327 nwalign.c:2633:14: error: assignment to ‘PyObject *’ {aka ‘struct _object *’} from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 2025-09-07T20:28:42,327 2633 | __pyx_v_ai = PyString_FromStringAndSize(NULL, __pyx_v_seqlen); 2025-09-07T20:28:42,327 | ^ 2025-09-07T20:28:42,330 nwalign.c:2642:14: error: assignment to ‘PyObject *’ {aka ‘struct _object *’} from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 2025-09-07T20:28:42,330 2642 | __pyx_v_aj = PyString_FromStringAndSize(NULL, __pyx_v_seqlen); 2025-09-07T20:28:42,330 | ^ 2025-09-07T20:28:42,354 nwalign.c:2651:21: error: implicit declaration of function ‘PyString_AS_STRING’; did you mean ‘PyBytes_AS_STRING’? [-Wimplicit-function-declaration] 2025-09-07T20:28:42,354 2651 | __pyx_v_align_j = PyString_AS_STRING(__pyx_v_aj); 2025-09-07T20:28:42,354 | ^~~~~~~~~~~~~~~~~~ 2025-09-07T20:28:42,354 | PyBytes_AS_STRING 2025-09-07T20:28:42,357 nwalign.c:2651:19: error: assignment to ‘char *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 2025-09-07T20:28:42,358 2651 | __pyx_v_align_j = PyString_AS_STRING(__pyx_v_aj); 2025-09-07T20:28:42,358 | ^ 2025-09-07T20:28:42,361 nwalign.c:2660:19: error: assignment to ‘char *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 2025-09-07T20:28:42,361 2660 | __pyx_v_align_i = PyString_AS_STRING(__pyx_v_ai); 2025-09-07T20:28:42,361 | ^ 2025-09-07T20:28:42,399 nwalign.c:2864:3: error: implicit declaration of function ‘_PyString_Resize’ [-Wimplicit-function-declaration] 2025-09-07T20:28:42,399 2864 | _PyString_Resize((&__pyx_v_aj), __pyx_v_align_counter); 2025-09-07T20:28:42,399 | ^~~~~~~~~~~~~~~~ 2025-09-07T20:28:42,402 nwalign.c:1435:14: warning: variable ‘__pyx_bshape_1_agap’ set but not used [-Wunused-but-set-variable] 2025-09-07T20:28:42,402 1435 | Py_ssize_t __pyx_bshape_1_agap = 0; 2025-09-07T20:28:42,402 | ^~~~~~~~~~~~~~~~~~~ 2025-09-07T20:28:42,403 nwalign.c:1434:14: warning: variable ‘__pyx_bshape_0_agap’ set but not used [-Wunused-but-set-variable] 2025-09-07T20:28:42,403 1434 | Py_ssize_t __pyx_bshape_0_agap = 0; 2025-09-07T20:28:42,403 | ^~~~~~~~~~~~~~~~~~~ 2025-09-07T20:28:42,404 nwalign.c:1430:14: warning: variable ‘__pyx_bshape_1_score’ set but not used [-Wunused-but-set-variable] 2025-09-07T20:28:42,405 1430 | Py_ssize_t __pyx_bshape_1_score = 0; 2025-09-07T20:28:42,405 | ^~~~~~~~~~~~~~~~~~~~ 2025-09-07T20:28:42,406 nwalign.c:1429:14: warning: variable ‘__pyx_bshape_0_score’ set but not used [-Wunused-but-set-variable] 2025-09-07T20:28:42,406 1429 | Py_ssize_t __pyx_bshape_0_score = 0; 2025-09-07T20:28:42,406 | ^~~~~~~~~~~~~~~~~~~~ 2025-09-07T20:28:42,407 nwalign.c:1425:14: warning: variable ‘__pyx_bshape_1_pointer’ set but not used [-Wunused-but-set-variable] 2025-09-07T20:28:42,407 1425 | Py_ssize_t __pyx_bshape_1_pointer = 0; 2025-09-07T20:28:42,407 | ^~~~~~~~~~~~~~~~~~~~~~ 2025-09-07T20:28:42,409 nwalign.c:1424:14: warning: variable ‘__pyx_bshape_0_pointer’ set but not used [-Wunused-but-set-variable] 2025-09-07T20:28:42,409 1424 | Py_ssize_t __pyx_bshape_0_pointer = 0; 2025-09-07T20:28:42,409 | ^~~~~~~~~~~~~~~~~~~~~~ 2025-09-07T20:28:42,410 nwalign.c:1420:14: warning: variable ‘__pyx_bshape_1_amatrix’ set but not used [-Wunused-but-set-variable] 2025-09-07T20:28:42,410 1420 | Py_ssize_t __pyx_bshape_1_amatrix = 0; 2025-09-07T20:28:42,410 | ^~~~~~~~~~~~~~~~~~~~~~ 2025-09-07T20:28:42,411 nwalign.c:1419:14: warning: variable ‘__pyx_bshape_0_amatrix’ set but not used [-Wunused-but-set-variable] 2025-09-07T20:28:42,411 1419 | Py_ssize_t __pyx_bshape_0_amatrix = 0; 2025-09-07T20:28:42,411 | ^~~~~~~~~~~~~~~~~~~~~~ 2025-09-07T20:28:42,419 nwalign.c: In function ‘__pyx_pf_7nwalign_main’: 2025-09-07T20:28:42,422 nwalign.c:3164:13: error: assignment to ‘PyObject *’ {aka ‘struct _object *’} from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 2025-09-07T20:28:42,422 3164 | __pyx_t_2 = PyEval_CallObjectWithKeywords(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), ((PyObject *)__pyx_1)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 252; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-07T20:28:42,422 | ^ 2025-09-07T20:28:42,427 nwalign.c:3192:13: error: assignment to ‘PyObject *’ {aka ‘struct _object *’} from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 2025-09-07T20:28:42,427 3192 | __pyx_t_3 = PyEval_CallObjectWithKeywords(__pyx_t_2, ((PyObject *)__pyx_t_1), ((PyObject *)__pyx_1)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 255; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-07T20:28:42,427 | ^ 2025-09-07T20:28:42,432 nwalign.c:3219:13: error: assignment to ‘PyObject *’ {aka ‘struct _object *’} from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 2025-09-07T20:28:42,432 3219 | __pyx_t_2 = PyEval_CallObjectWithKeywords(__pyx_t_3, ((PyObject *)__pyx_t_1), ((PyObject *)__pyx_1)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 256; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-07T20:28:42,432 | ^ 2025-09-07T20:28:42,437 nwalign.c:3246:13: error: assignment to ‘PyObject *’ {aka ‘struct _object *’} from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 2025-09-07T20:28:42,437 3246 | __pyx_t_3 = PyEval_CallObjectWithKeywords(__pyx_t_2, ((PyObject *)__pyx_t_1), ((PyObject *)__pyx_1)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 257; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-07T20:28:42,437 | ^ 2025-09-07T20:28:42,441 nwalign.c:3273:13: error: assignment to ‘PyObject *’ {aka ‘struct _object *’} from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 2025-09-07T20:28:42,441 3273 | __pyx_t_2 = PyEval_CallObjectWithKeywords(__pyx_t_3, ((PyObject *)__pyx_t_1), ((PyObject *)__pyx_1)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 258; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-07T20:28:42,441 | ^ 2025-09-07T20:28:42,446 nwalign.c:3307:13: error: assignment to ‘PyObject *’ {aka ‘struct _object *’} from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 2025-09-07T20:28:42,446 3307 | __pyx_t_3 = PyEval_CallObjectWithKeywords(__pyx_t_2, ((PyObject *)__pyx_t_1), ((PyObject *)__pyx_1)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 259; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-07T20:28:42,446 | ^ 2025-09-07T20:28:42,479 nwalign.c: In function ‘__pyx_pf_5numpy_7ndarray___getbuffer__’: 2025-09-07T20:28:42,485 nwalign.c:3646:69: error: ‘NPY_C_CONTIGUOUS’ undeclared (first use in this function); did you mean ‘PyBUF_C_CONTIGUOUS’? 2025-09-07T20:28:42,485 3646 | __pyx_t_1 = (!PyArray_CHKFLAGS(((PyArrayObject *)__pyx_v_self), NPY_C_CONTIGUOUS)); 2025-09-07T20:28:42,485 | ^~~~~~~~~~~~~~~~ 2025-09-07T20:28:42,485 | PyBUF_C_CONTIGUOUS 2025-09-07T20:28:42,485 nwalign.c:3646:69: note: each undeclared identifier is reported only once for each function it appears in 2025-09-07T20:28:42,512 nwalign.c:3690:69: error: ‘NPY_F_CONTIGUOUS’ undeclared (first use in this function); did you mean ‘PyBUF_F_CONTIGUOUS’? 2025-09-07T20:28:42,512 3690 | __pyx_t_1 = (!PyArray_CHKFLAGS(((PyArrayObject *)__pyx_v_self), NPY_F_CONTIGUOUS)); 2025-09-07T20:28:42,512 | ^~~~~~~~~~~~~~~~ 2025-09-07T20:28:42,512 | PyBUF_F_CONTIGUOUS 2025-09-07T20:28:42,516 nwalign.c: In function ‘__pyx_f_5numpy__util_dtypestring’: 2025-09-07T20:28:42,521 nwalign.c:4316:45: error: ‘PyArray_Descr’ {aka ‘struct _PyArray_Descr’} has no member named ‘fields’ 2025-09-07T20:28:42,521 4316 | __pyx_t_2 = PyObject_GetAttr(__pyx_v_descr->fields, __pyx_kp_itervalues); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 254; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-07T20:28:42,521 | ^~ 2025-09-07T20:28:42,558 nwalign.c: In function ‘__Pyx_ErrRestore’: 2025-09-07T20:28:42,567 nwalign.c:5306:18: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘exc_state’? 2025-09-07T20:28:42,567 5306 | if ((tstate->exc_type != NULL) & (tstate->exc_type != Py_None)) { 2025-09-07T20:28:42,567 | ^~~~~~~~ 2025-09-07T20:28:42,567 | exc_state 2025-09-07T20:28:42,576 nwalign.c:5306:47: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘exc_state’? 2025-09-07T20:28:42,576 5306 | if ((tstate->exc_type != NULL) & (tstate->exc_type != Py_None)) { 2025-09-07T20:28:42,576 | ^~~~~~~~ 2025-09-07T20:28:42,576 | exc_state 2025-09-07T20:28:42,585 nwalign.c:5307:28: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘exc_state’? 2025-09-07T20:28:42,585 5307 | tmp_type = tstate->exc_type; 2025-09-07T20:28:42,585 | ^~~~~~~~ 2025-09-07T20:28:42,585 | exc_state 2025-09-07T20:28:42,591 nwalign.c:5308:27: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’ 2025-09-07T20:28:42,591 5308 | tmp_value = tstate->exc_value; 2025-09-07T20:28:42,591 | ^~ 2025-09-07T20:28:42,597 nwalign.c:5309:24: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’ 2025-09-07T20:28:42,597 5309 | tmp_tb = tstate->exc_traceback; 2025-09-07T20:28:42,597 | ^~ 2025-09-07T20:28:42,606 nwalign.c:5312:17: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘exc_state’? 2025-09-07T20:28:42,606 5312 | tstate->exc_type = 0; 2025-09-07T20:28:42,606 | ^~~~~~~~ 2025-09-07T20:28:42,606 | exc_state 2025-09-07T20:28:42,612 nwalign.c:5313:15: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’ 2025-09-07T20:28:42,612 5313 | tstate->exc_value = 0; 2025-09-07T20:28:42,612 | ^~ 2025-09-07T20:28:42,618 nwalign.c:5314:15: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’ 2025-09-07T20:28:42,618 5314 | tstate->exc_traceback = 0; 2025-09-07T20:28:42,618 | ^~ 2025-09-07T20:28:42,624 nwalign.c:5321:22: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_type’ 2025-09-07T20:28:42,624 5321 | tmp_type = tstate->curexc_type; 2025-09-07T20:28:42,624 | ^~ 2025-09-07T20:28:42,630 nwalign.c:5322:23: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_value’ 2025-09-07T20:28:42,630 5322 | tmp_value = tstate->curexc_value; 2025-09-07T20:28:42,630 | ^~ 2025-09-07T20:28:42,636 nwalign.c:5323:20: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_traceback’ 2025-09-07T20:28:42,636 5323 | tmp_tb = tstate->curexc_traceback; 2025-09-07T20:28:42,637 | ^~ 2025-09-07T20:28:42,642 nwalign.c:5324:11: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_type’ 2025-09-07T20:28:42,642 5324 | tstate->curexc_type = type; 2025-09-07T20:28:42,643 | ^~ 2025-09-07T20:28:42,648 nwalign.c:5325:11: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_value’ 2025-09-07T20:28:42,649 5325 | tstate->curexc_value = value; 2025-09-07T20:28:42,649 | ^~ 2025-09-07T20:28:42,655 nwalign.c:5326:11: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_traceback’ 2025-09-07T20:28:42,655 5326 | tstate->curexc_traceback = tb; 2025-09-07T20:28:42,655 | ^~ 2025-09-07T20:28:42,655 nwalign.c: In function ‘__Pyx_ErrFetch’: 2025-09-07T20:28:42,661 nwalign.c:5334:19: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_type’ 2025-09-07T20:28:42,661 5334 | *type = tstate->curexc_type; 2025-09-07T20:28:42,661 | ^~ 2025-09-07T20:28:42,667 nwalign.c:5335:20: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_value’ 2025-09-07T20:28:42,667 5335 | *value = tstate->curexc_value; 2025-09-07T20:28:42,667 | ^~ 2025-09-07T20:28:42,673 nwalign.c:5336:17: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_traceback’ 2025-09-07T20:28:42,673 5336 | *tb = tstate->curexc_traceback; 2025-09-07T20:28:42,673 | ^~ 2025-09-07T20:28:42,679 nwalign.c:5338:11: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_type’ 2025-09-07T20:28:42,679 5338 | tstate->curexc_type = 0; 2025-09-07T20:28:42,679 | ^~ 2025-09-07T20:28:42,685 nwalign.c:5339:11: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_value’ 2025-09-07T20:28:42,685 5339 | tstate->curexc_value = 0; 2025-09-07T20:28:42,686 | ^~ 2025-09-07T20:28:42,691 nwalign.c:5340:11: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_traceback’ 2025-09-07T20:28:42,692 5340 | tstate->curexc_traceback = 0; 2025-09-07T20:28:42,692 | ^~ 2025-09-07T20:28:42,733 nwalign.c: In function ‘__Pyx_ParseOptionalKeywords’: 2025-09-07T20:28:42,742 nwalign.c:5531:25: error: implicit declaration of function ‘PyUnicode_GET_SIZE’; did you mean ‘PyDict_GET_SIZE’? [-Wimplicit-function-declaration] 2025-09-07T20:28:42,742 5531 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2025-09-07T20:28:42,742 | ^~~~~~~~~~~~~~~~~~ 2025-09-07T20:28:42,743 | PyDict_GET_SIZE 2025-09-07T20:28:42,745 nwalign.c: In function ‘__Pyx_GetException’: 2025-09-07T20:28:42,751 nwalign.c:5585:19: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_type’ 2025-09-07T20:28:42,751 5585 | *type = tstate->curexc_type; 2025-09-07T20:28:42,751 | ^~ 2025-09-07T20:28:42,757 nwalign.c:5586:20: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_value’ 2025-09-07T20:28:42,757 5586 | *value = tstate->curexc_value; 2025-09-07T20:28:42,757 | ^~ 2025-09-07T20:28:42,763 nwalign.c:5587:17: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_traceback’ 2025-09-07T20:28:42,763 5587 | *tb = tstate->curexc_traceback; 2025-09-07T20:28:42,763 | ^~ 2025-09-07T20:28:42,769 nwalign.c:5588:11: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_type’ 2025-09-07T20:28:42,770 5588 | tstate->curexc_type = 0; 2025-09-07T20:28:42,770 | ^~ 2025-09-07T20:28:42,776 nwalign.c:5589:11: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_value’ 2025-09-07T20:28:42,776 5589 | tstate->curexc_value = 0; 2025-09-07T20:28:42,776 | ^~ 2025-09-07T20:28:42,782 nwalign.c:5590:11: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_traceback’ 2025-09-07T20:28:42,782 5590 | tstate->curexc_traceback = 0; 2025-09-07T20:28:42,782 | ^~ 2025-09-07T20:28:42,793 nwalign.c:5597:24: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘exc_state’? 2025-09-07T20:28:42,793 5597 | tmp_type = tstate->exc_type; 2025-09-07T20:28:42,793 | ^~~~~~~~ 2025-09-07T20:28:42,793 | exc_state 2025-09-07T20:28:42,799 nwalign.c:5598:23: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’ 2025-09-07T20:28:42,799 5598 | tmp_value = tstate->exc_value; 2025-09-07T20:28:42,799 | ^~ 2025-09-07T20:28:42,805 nwalign.c:5599:20: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’ 2025-09-07T20:28:42,805 5599 | tmp_tb = tstate->exc_traceback; 2025-09-07T20:28:42,805 | ^~ 2025-09-07T20:28:42,814 nwalign.c:5600:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘exc_state’? 2025-09-07T20:28:42,814 5600 | tstate->exc_type = *type; 2025-09-07T20:28:42,814 | ^~~~~~~~ 2025-09-07T20:28:42,814 | exc_state 2025-09-07T20:28:42,820 nwalign.c:5601:11: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’ 2025-09-07T20:28:42,820 5601 | tstate->exc_value = *value; 2025-09-07T20:28:42,820 | ^~ 2025-09-07T20:28:42,826 nwalign.c:5602:11: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’ 2025-09-07T20:28:42,826 5602 | tstate->exc_traceback = *tb; 2025-09-07T20:28:42,826 | ^~ 2025-09-07T20:28:42,826 nwalign.c: In function ‘__Pyx_ExceptionSave’: 2025-09-07T20:28:42,835 nwalign.c:5619:21: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘exc_state’? 2025-09-07T20:28:42,835 5619 | *type = tstate->exc_type; 2025-09-07T20:28:42,835 | ^~~~~~~~ 2025-09-07T20:28:42,836 | exc_state 2025-09-07T20:28:42,841 nwalign.c:5620:20: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’ 2025-09-07T20:28:42,842 5620 | *value = tstate->exc_value; 2025-09-07T20:28:42,842 | ^~ 2025-09-07T20:28:42,848 nwalign.c:5621:17: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’ 2025-09-07T20:28:42,848 5621 | *tb = tstate->exc_traceback; 2025-09-07T20:28:42,848 | ^~ 2025-09-07T20:28:42,848 nwalign.c: In function ‘__Pyx_ExceptionReset’: 2025-09-07T20:28:42,857 nwalign.c:5630:24: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘exc_state’? 2025-09-07T20:28:42,857 5630 | tmp_type = tstate->exc_type; 2025-09-07T20:28:42,857 | ^~~~~~~~ 2025-09-07T20:28:42,857 | exc_state 2025-09-07T20:28:42,863 nwalign.c:5631:23: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’ 2025-09-07T20:28:42,863 5631 | tmp_value = tstate->exc_value; 2025-09-07T20:28:42,863 | ^~ 2025-09-07T20:28:42,869 nwalign.c:5632:20: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’ 2025-09-07T20:28:42,869 5632 | tmp_tb = tstate->exc_traceback; 2025-09-07T20:28:42,869 | ^~ 2025-09-07T20:28:42,878 nwalign.c:5633:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘exc_state’? 2025-09-07T20:28:42,878 5633 | tstate->exc_type = type; 2025-09-07T20:28:42,878 | ^~~~~~~~ 2025-09-07T20:28:42,878 | exc_state 2025-09-07T20:28:42,884 nwalign.c:5634:11: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’ 2025-09-07T20:28:42,884 5634 | tstate->exc_value = value; 2025-09-07T20:28:42,884 | ^~ 2025-09-07T20:28:42,890 nwalign.c:5635:11: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’ 2025-09-07T20:28:42,890 5635 | tstate->exc_traceback = tb; 2025-09-07T20:28:42,891 | ^~ 2025-09-07T20:28:42,950 nwalign.c: In function ‘__Pyx_AddTraceback’: 2025-09-07T20:28:42,957 nwalign.c:6318:5: warning: ‘PyCode_New’ is deprecated [-Wdeprecated-declarations] 2025-09-07T20:28:42,957 6318 | py_code = PyCode_New( 2025-09-07T20:28:42,958 | ^~~~~~~ 2025-09-07T20:28:42,958 In file included from /usr/include/python3.13/Python.h:101, 2025-09-07T20:28:42,958 from nwalign.c:4: 2025-09-07T20:28:42,958 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-07T20:28:42,958 213 | PyCode_New( 2025-09-07T20:28:42,958 | ^~~~~~~~~~ 2025-09-07T20:28:42,965 nwalign.c:6334:9: error: passing argument 14 of ‘PyCode_New’ makes pointer from integer without a cast [-Wint-conversion] 2025-09-07T20:28:42,965 6334 | __pyx_lineno, /*int firstlineno,*/ 2025-09-07T20:28:42,965 | ^~~~~~~~~~~~ 2025-09-07T20:28:42,965 | | 2025-09-07T20:28:42,965 | int 2025-09-07T20:28:42,965 /usr/include/python3.13/cpython/code.h:216:45: note: expected ‘PyObject *’ {aka ‘struct _object *’} but argument is of type ‘int’ 2025-09-07T20:28:42,965 216 | PyObject *l, PyObject *m, PyObject *n, int o, PyObject *p, 2025-09-07T20:28:42,965 | ~~~~~~~~~~^ 2025-09-07T20:28:42,972 nwalign.c:6335:9: error: passing argument 15 of ‘PyCode_New’ makes integer from pointer without a cast [-Wint-conversion] 2025-09-07T20:28:42,972 6335 | empty_string /*PyObject *lnotab*/ 2025-09-07T20:28:42,972 | ^~~~~~~~~~~~ 2025-09-07T20:28:42,972 | | 2025-09-07T20:28:42,972 | PyObject * {aka struct _object *} 2025-09-07T20:28:42,972 /usr/include/python3.13/cpython/code.h:216:52: note: expected ‘int’ but argument is of type ‘PyObject *’ {aka ‘struct _object *’} 2025-09-07T20:28:42,972 216 | PyObject *l, PyObject *m, PyObject *n, int o, PyObject *p, 2025-09-07T20:28:42,972 | ~~~~^ 2025-09-07T20:28:42,979 nwalign.c:6318:15: error: too few arguments to function ‘PyCode_New’ 2025-09-07T20:28:42,979 6318 | py_code = PyCode_New( 2025-09-07T20:28:42,979 | ^~~~~~~~~~ 2025-09-07T20:28:42,979 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-07T20:28:42,980 213 | PyCode_New( 2025-09-07T20:28:42,980 | ^~~~~~~~~~ 2025-09-07T20:28:42,989 nwalign.c:6345:13: error: invalid use of incomplete typedef ‘PyFrameObject’ {aka ‘struct _frame’} 2025-09-07T20:28:42,989 6345 | py_frame->f_lineno = __pyx_lineno; 2025-09-07T20:28:42,989 | ^~ 2025-09-07T20:28:43,059 nwalign.c: At top level: 2025-09-07T20:28:43,064 nwalign.c:4232:13: warning: ‘__pyx_pf_5numpy_7ndarray___releasebuffer__’ defined but not used [-Wunused-function] 2025-09-07T20:28:43,064 4232 | static void __pyx_pf_5numpy_7ndarray___releasebuffer__(PyObject *__pyx_v_self, Py_buffer *__pyx_v_info) { 2025-09-07T20:28:43,064 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-07T20:28:43,068 nwalign.c:3569:12: warning: ‘__pyx_pf_5numpy_7ndarray___getbuffer__’ defined but not used [-Wunused-function] 2025-09-07T20:28:43,069 3569 | static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyObject *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags) { 2025-09-07T20:28:43,069 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-07T20:28:43,074 error: command '/usr/bin/arm-linux-gnueabihf-gcc' failed with exit code 1 2025-09-07T20:28:43,246 ERROR: python setup.py bdist_wheel exited with 1 2025-09-07T20:28:43,259 [bold magenta]full command[/]: [blue]/usr/bin/python3 -u -c ' 2025-09-07T20:28:43,259 exec(compile('"'"''"'"''"'"' 2025-09-07T20:28:43,259 # This is -- a caller that pip uses to run setup.py 2025-09-07T20:28:43,259 # 2025-09-07T20:28:43,259 # - It imports setuptools before invoking setup.py, to enable projects that directly 2025-09-07T20:28:43,259 # import from `distutils.core` to work with newer packaging standards. 2025-09-07T20:28:43,259 # - It provides a clear error message when setuptools is not installed. 2025-09-07T20:28:43,259 # - It sets `sys.argv[0]` to the underlying `setup.py`, when invoking `setup.py` so 2025-09-07T20:28:43,259 # setuptools doesn'"'"'t think the script is `-c`. This avoids the following warning: 2025-09-07T20:28:43,259 # manifest_maker: standard file '"'"'-c'"'"' not found". 2025-09-07T20:28:43,259 # - It generates a shim setup.py, for handling setup.cfg-only projects. 2025-09-07T20:28:43,259 import os, sys, tokenize, traceback 2025-09-07T20:28:43,259 2025-09-07T20:28:43,259 try: 2025-09-07T20:28:43,259 import setuptools 2025-09-07T20:28:43,259 except ImportError: 2025-09-07T20:28:43,259 print( 2025-09-07T20:28:43,259 "ERROR: Can not execute `setup.py` since setuptools failed to import in " 2025-09-07T20:28:43,259 "the build environment with exception:", 2025-09-07T20:28:43,259 file=sys.stderr, 2025-09-07T20:28:43,259 ) 2025-09-07T20:28:43,259 traceback.print_exc() 2025-09-07T20:28:43,259 sys.exit(1) 2025-09-07T20:28:43,259 2025-09-07T20:28:43,259 __file__ = %r 2025-09-07T20:28:43,259 sys.argv[0] = __file__ 2025-09-07T20:28:43,259 2025-09-07T20:28:43,259 if os.path.exists(__file__): 2025-09-07T20:28:43,259 filename = __file__ 2025-09-07T20:28:43,259 with tokenize.open(__file__) as f: 2025-09-07T20:28:43,259 setup_py_code = f.read() 2025-09-07T20:28:43,259 else: 2025-09-07T20:28:43,259 filename = "" 2025-09-07T20:28:43,259 setup_py_code = "from setuptools import setup; setup()" 2025-09-07T20:28:43,259 2025-09-07T20:28:43,259 exec(compile(setup_py_code, filename, "exec")) 2025-09-07T20:28:43,259 '"'"''"'"''"'"' % ('"'"'/tmp/pip-wheel-jmlhl5rb/nwalign_0f5f0cbb29734c8d8106745a44654ca4/setup.py'"'"',), "", "exec"))' bdist_wheel -d /tmp/pip-wheel-vxa1tynf[/] 2025-09-07T20:28:43,259 [bold magenta]cwd[/]: /tmp/pip-wheel-jmlhl5rb/nwalign_0f5f0cbb29734c8d8106745a44654ca4/ 2025-09-07T20:28:43,259 Building wheel for nwalign (setup.py): finished with status 'error' 2025-09-07T20:28:43,260 ERROR: Failed building wheel for nwalign 2025-09-07T20:28:43,260 Running setup.py clean for nwalign 2025-09-07T20:28:43,261 Running command python setup.py clean 2025-09-07T20:28:44,166 /usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'test_suite' 2025-09-07T20:28:44,166 warnings.warn(msg) 2025-09-07T20:28:44,554 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-07T20:28:44,554 !! 2025-09-07T20:28:44,554 ******************************************************************************** 2025-09-07T20:28:44,554 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-07T20:28:44,555 License :: OSI Approved :: BSD License 2025-09-07T20:28:44,555 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-07T20:28:44,555 ******************************************************************************** 2025-09-07T20:28:44,555 !! 2025-09-07T20:28:44,555 self._finalize_license_expression() 2025-09-07T20:28:44,630 running clean 2025-09-07T20:28:44,777 removing 'build/temp.linux-armv7l-cpython-313' (and everything under it) 2025-09-07T20:28:44,777 'build/lib.linux-armv7l-cpython-313' does not exist -- can't clean it 2025-09-07T20:28:44,777 'build/bdist.linux-armv7l' does not exist -- can't clean it 2025-09-07T20:28:44,778 'build/scripts-3.13' does not exist -- can't clean it 2025-09-07T20:28:44,778 removing 'build' 2025-09-07T20:28:44,916 Failed to build nwalign 2025-09-07T20:28:44,916 ERROR: Failed to build one or more wheels 2025-09-07T20:28:44,917 Exception information: 2025-09-07T20:28:44,917 Traceback (most recent call last): 2025-09-07T20:28:44,917 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 105, in _run_wrapper 2025-09-07T20:28:44,917 status = _inner_run() 2025-09-07T20:28:44,917 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 96, in _inner_run 2025-09-07T20:28:44,917 return self.run(options, args) 2025-09-07T20:28:44,917 ~~~~~~~~^^^^^^^^^^^^^^^ 2025-09-07T20:28:44,917 File "/usr/lib/python3/dist-packages/pip/_internal/cli/req_command.py", line 68, in wrapper 2025-09-07T20:28:44,917 return func(self, options, args) 2025-09-07T20:28:44,917 File "/usr/lib/python3/dist-packages/pip/_internal/commands/wheel.py", line 180, in run 2025-09-07T20:28:44,917 raise CommandError("Failed to build one or more wheels") 2025-09-07T20:28:44,917 pip._internal.exceptions.CommandError: Failed to build one or more wheels 2025-09-07T20:28:44,921 Removed build tracker: '/tmp/pip-build-tracker-kopn3982'